First off let me say thanks for all the help i have gotten over the years for my jeep.

Symptoms:
Unreliable starting. Sometimes it will start right up and others i can sit there and crank it all day and nothing will happen. Sometimes it does it when its hot (100+) sometimes when its cooler (~75)

and now my mechanic is telling me that there is a short in the wiring harness and to fix it we will need to replace the whole thing. I can't find any information about how much a part will cost and then how to replace it. I prefer to to the work myself, but just out of college my tool selection is greatly limited.

How much is a wiring harness for a 96 ZJ? where do i find one? How long and hard to replace it?

It's very unlikely you need a wiring harness. If you do need a harness, it will have to come from a salvage yard. I would make the mechanic tell me why exactly I need a wiring harness.

Are you missing spark or fuel? If you have both and it doesnt crank, given the things you have replaced, I would look very carefully at the cam sensor and connector. The connector has given me problems where it didnt want to crank until i unplugged it and plugged back in. Then I used a sharp point to elongate the sockets so they would hold the pins better. No problems since.

I'm going to say yes... My wiring harness had an unfortunate run in with a sawzall, I spliced about 12 wires back together and i havent noticed any ill effects yet.

If you want to be completely anal about it, I would imagine, depending on which wire(s) are the culprit, that you could replace the entire wire pin to pin, with enough patience, of course this becomes less practical as the number of wires increase

UPDATE:
So my new mechanic I took my car to has identified the problem. Not a short so i will update the thread title. When I took it in to my ususal mechanic and had the cat replaced, they put an new one in that was too small. This increased the backpressure on my cylinders and was preventing it from starting and causing it to die while running. The mechanic bypassed the cat (for diagnositc purposes, removing or tampering with any part of the emissions control is illegal and not condoned by this forum) and she fired up right away and ran like new!